Are you talking about Obito with both Mangekyou, or the cannon Obito with one Mangekyou and some Hashirama cells? Because all we've ever seen is him with the capacity to abuse his Hashirama stamina to spam his single MS ability; we have no idea what kinds of tradeoffs he'd have to make if he sacrificed that stamina and life force to obtain his full Doujutsu. Yes, he'd have access to Susano'o and the same Ranged Kamui as Kakashi, but he'd probably have gone blind eventually like every other MS user, and he wouldn't be able to phase through dimensions indefinitely. Eventually, he would run out of steam.
As it stands, Obito would still struggle to land a hit against Itachi as long as Itachi can maintain Susano'o. A Sharingan user like Itachi has very solid reflexes, and so landing either version of Kamui would be difficult (even a clueless Deidara managed to avoid a lethal blow).
Likewise, while Itachi is the superior Genjutsu user, it is unlikely that any Genjutsu would hold Obito for more than a few seconds, aside from maybe Tsukuyomi. I don't see an MS user being one-shot by any MS Genjutsu other than perhaps Koto, and then only because Koto is undetectable.
I'd say Obito's best chance is actually in his Mokuton-enhanced form with a single MS, simply because he would have enough stamina to constantly evade Itachi's attacks and wear him down. Itachi would need to bait Obito into exposing himself if he wanted to land a lethal blow, and using any MS Jutsu is extremely taxing on Itachi (sick or healthy). Only Edo Itachi could hope to spam his MS enough to overwhelm Obito.
That said, Obito has no way of landing a hit on Itachi until Itachi becomes exhausted, and still needs to *feign* attacks in order to get Itachi to exhaust himself. In other words, Obito has to expose himself to risks to try and land a hit, and Itachi is the perfect ninja to capitalize on those and potentially win.
This is probably the reason why they never fought. Obito was content to control Nagato, the most powerful of the three.
Also relevant: Can the Gedo Mazou be defeated by Totsuka? I don't want to sound like one of the retarded Itachi fantrolls, but I actually think it might be vulnerable (although it has ranged attacks to keep Susano'o at bay).
